1. Field
The subject matter relates to a one-bead-one-sequence composition, a library of tagged chemicals comprising a plurality of one-bead-one-sequence compositions, a method for identifying a candidate molecule from a library of tagged chemicals, and a composition produced by a process, all as described herein.
2. Background
Pharmaceutical product pipelines and FDA approval rates have weakened dramatically over the past decade. Thus, to aid the discovery of new drugs, Applicants have developed a technology for processing and screening encoded chemical libraries.
State-of-the-Art in Achieving Molecular Recognition.
Currently, specific recognition of molecular targets is primarily achieved using monoclonal antibodies selected by hybridoma technology in which antibody-producing animal cells are hybridized with immortalized myeloma cells. To a much lesser extent, target-specific binding has been demonstrated using peptides selected by phage display or small molecule lead compounds selected by labor-intensive screening methods.
Conceptually, all screening technologies involve finding a “needle in a haystack” by exploiting some property of the needle not found in the rest of the haystack. Often in the prior art, this amounts to a trial-and-error testing of each candidate in the haystack. Ultrahigh-throughput methods allow practical implementation of the trial-and-error screening principle without undue time, expense, effort, and experimentation. However, different screening technologies have been shown to produce very different results in the candidates identified from a given library, and throughput remains inadequate to keep up with available library production capabilities. Therefore, much effort has been devoted to evaluate different screening methods and improve throughput by multiplexing, miniaturizing, and automating.
The three most widely used current methods of target-specific binding (antibodies, peptides, and small molecule pharmacophores) are each associated with their own unique challenges. For example, antibodies are complex proteins with variable glycosylation patterns and microheterogeneity at the antigen binding site. Peptides typically lack this heterogeneity, but share antibodies' sensitivity to extremes of pH and ionic strength. Small molecule lead compounds are chemically well-defined, stable and can be produced with very high purity. However, they are difficult to screen. What is needed is a method to rapidly and sensitively screen promising lead compounds from a large and diverse library of small molecules.
Clonal DNA-bead libraries are a novel improvement over current state-of-the-art products, such as the Clonal Single Molecule Array™ (CSMA) technology developed by Solexa, Inc. In CSMA, single molecules of DNA are attached to a flat surface. The surface is conjugated with PCR primers, and each single molecule of DNA is amplified by PCR to produce ˜1000 identical copies, achieving densities of ˜10 million clonal clusters per cm2 (1 clonal cluster per 10 μm2).
One approach for multiplexing and miniaturizing is to use tiny beads made of different plastics or glasses. These can be functionalized with a range of fluorescent dyes, small molecules and magnetic (or paramagnetic) particles. Beads functionalized in this way can serve both as “handles” and “tags” for small molecule lead compounds and drug candidates during the screening process.
Three primary obstacles stand in the way of using beads to screen small molecule libraries. First, one must find a way to attach enough of the small molecules to the beads in order to generate a detectable signal of the desired functional property. Second, each bead must have only one type of small molecule attached to it so as to avoid attenuating the signal or confounding it with cross-talk. Third, the signal must be processed to convey the identity of the small molecule; when a target-binding bead is detected, its corresponding small molecule is efficiently identified, characterized, and synthesized.